Bio Test 2

Created by JennBadding 

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morphology

the shape and appearance of an organisms body and its component parts

phylogeny

Evolutionary history of a group of organisms

chromosome

A single piece of coiled DNA and associated proteins found in linear forms in the nucleus of eukaryotic cells and circular forms in the cytoplasm of prokaryotic cells; contains genes that encode traits. Each species has a characteristic number of chromosomes.

genes

a section of DNA (or RNA, for some viruses) that encodes information for building one or more related polypeptides or functional RNA molecules along with the regulatory sequences required for its transcription

nucleoid

Area in prokaryotic cells in which DNA is concentrated, though not bounded by a membrane

plasmids

a small, usually circular, supercoiled DNA molecule independent of the cells' main chromosome(s) in prokaryotes and some eukaryotes

ribosomes

a large macromolecular machine that synthesizes proteins by suing the generic information encoded in messenger RNA. Consists of two subunits, each composed of ribosomal RNA and proteins

organelles

A membrane-enclosed structure with a specialized function within a cell.

cytoskeleton

A network of microtubules, microfilaments, and intermediate filaments that branch throughout the cytoplasm and serve a variety of mechanical and transport functions.

cell wall

A rigid structure that surrounds the cell membrane and provides support to the cell

cytoplasm

Contents (formation) of the cell (apart from the nucleus and cell membrane).

glycolipids

any lipid molecule that is covalently bonded to a carbohydrate group

flagella

a long, cellular projection that undulates (in eukaryotes) or rotates (in prokaryotes) to move the cell through an aqueous environment

fimbriae

a long needlelike projection from the cell membrane of prokaryotes that is involved in attachment to nonliving surfaces or other cells

cytosol

fluid portion of the cytoplasm, excluding the contents of membrane-enclosed organelles

Compartmentalization also offers two key advantages:

1. incompatible chemical reactions can be separated
2. Chemical reactions become more efficient

Eukaryotic cells vs prokaryotic

1. Eukaryotic chromosoms are found inside a membrane-bound compartment calle dthe nucleus.
2. eukartyotic cells are often much larger than prokaryotes
3. eurkaryotic cells contain extensive amounts of internal membrane
4. eukaryotic cells feature a particularly diverse and dynamic cytoskelteon

nucleus

1) the center of the atom containing protons and neutrons
2) in eukaryotic cells, the large organelle containing the chromosomes and surrounded by a double membrane
3)a discrete clump of neuron cell bodies in the brain, usually sharing a distinct function

nuclear envelope

A double membrane that surrounds the nucleus in the cell

nuclear lamina

a lattice-like sheet of fibrous nuclear laminas, which are one type of intermediate filament. lines the inner membrane of the nuclear envelope, stiffening the envelope and helping to organize the chromosomes

endoplasmic reticulum

a network of interconnected membrane sacs and tubules found inside eukaryotic cells

rough endoplasmic reticulum RER

the portion of the endoplasmic reticulum that is dotted with ribosomes. involved in synthesis of plasma membrane proteins, secreted proteins, and proteins localized to the ER, Golgi apparatus, and lysosomes.

lumen

the interior space of any hollow structure or organ

Smooth endoplasmic reticulum SER

the portion of the ER that does not have ribosomes attached to it. involved in synthesis and secretion of lipids

Golgi apparatus

a eukaryotic organelle, consisting of stacks of flattened membranous sacs (cisternae), that function in processing and sorting proteins and lipids destined to be secreted or directed to other organelles.

cisternae

flattened, membrane-bound compartments that make up the Golgi apparatus

lysosomes

a small, acidified organelle in an animal cell containing enzymes that catalyze hydrolysis reactions and can digest large molecules

endomembrane system

a system of organelles in eukaryotic cells that synthesizes, processes, transports, and recycles proteins and lipids. Includes the endoplasmic reticulum (ER), Golgi apparatus, and lysosomes

peroxisomes

an organelle found in most eukaryotic cells that contains enzymes for oxidizing fatty acids and other compounds, including many toxins, rendering them harmless

glyoxysomes

specialized type of peroxisome found in plant cells and packed with enzymes for processing the products of photosynthesis

mitochondria

a eukaryotic organelle that is bounded by a double membrane and is the site of aerobic respiration and ATP synthesis

thylakoids

a membrane-bound network of flattened sac-like structures inside a plant chloroplast that function in converting light energy to chemical energy. a stack of thylakoid discs is a granum

grana

in chloroplasts, a stack of flattened, membrane-bound thylakoid discs where the light reactions of photosynthesis occur

stroma

the fluid matrix of a chloroplast in which the thylakoids are embedded. site where the Calvin cycle reactions occur

endosymbiosis theory

the theory that mitochondria and chloroplast evolved from prokaryotes that were engulfed by host cells and took up a symbiotic existence within those cells, a process termed primary endosymbiosis. In some eukaryotes, chloroplasts may have originated by secondary endosymbiosis; that is, when a cell engulfed a chloroplast-containing protist and retained its chloroplasts

differential centrifugation

procedure for separating cellular componenets according to their size and density by spinning a cell homogenate in a series of centrifuge runs. After each run, the supernatant is removed from the deposited material (pellet0 and spun again at progressively higher speeds

nuclear pores

an opening in the nuclear envelope that connects the inside of the nucleus with the cytoplasm and through which molecules such as mRNA and some proteins can pass

nuclear pore complex

a large complex of dozens of proteins lining a nuclear pore, defining its shape and regulating transport through the pore

ribosomal RNAs

RNA molecules that, together with proteins, make up ribosomes; the most abundant type of RNA.

messenger RNAs (mRNA)

an RNA molecule transcribed from DNA that carries information (in codons) that specifies the amino acid sequence of a polypeptide

nuclear localization signal (NLS)

a short amino acid sequence that marks a protein for delivery to the nucleus

pulse-chase experiment

A type of experiment in which a population of cells or molecules at a particular moment in time is marked by means of a labeled molecule and then their fate is followed over time.

culture

in cell biology, a collection of cells or a tissue growing under controlled conditions, usually in suspension or on the surface of a dish of solid growth medium

ER singal sequence

a short amino acid sequence that marks a polypeptide for transport to the endoplasmic reticulum, where synthesis of the polypeptide chain is completed and the signal sequence removed

signal recognition particle (SRP)

A RNA protein complex that binds to the ER signal sequence in polypeptide as it emerges from a ribosome and transports the ribosome-polypeptide complex to the ER membrane where synthesis of the polypeptide is completed. The ribosome + signal sequence + SRP complex then attaches to an SRP receptor in the ER membrane itself

cisternal maturation

the process of cargo movement through the Golgi apparatus by residing in cisternae that mature from cis to trans via the import and export of different Golgi enzymes

endocytosis

general term for any pinching off of the plasma membrane that results in the uptake of material from outside the cell. Includes phagocytosis, pinocytosis, and receptor-mediated endocytosis

receptor-mediated endocytosis

uptake by a cell of certain extracellular macromolecules, bound to specific receptors in the plasma membrane, by pinching of the membrane to form small membrane-bound vesicles

early endosome

a small transient organelle that is formed by the accumulation of vesicles from receptor-mediated endocytosis and is an early stage in the formation of a lysosome

late endosome

a membrane-bound vesicle that arises from an early endosome, accepts lysosomal enzymes from the Golgi, and matures into a lysosome

autopahgy

the process by which damaged organelles are surrounded by a membrane and delivered to a lysosome to be recycled

phagocytosis

uptake by a cell of small particles or cells by invagination and pinching off of the plasma membrane to form small, membrane-bound vesicles; one type of endocytosis

bulk-phase endocytosis

nonspecific uptake of extracellular fluid by pinching off the plasma membrane to form small membrane-bound vesicles; considered to be a means of retrieving membranes from the surface following exocytosis

actin filaments

a long fiber, about 7nm in diameter, composed of two intertwined strands of polymerized actin protein; one of the three types of cytoskeletal fibers. Involved in cell movement. Also called microfilament

motor protein

a class of proteins whose major function is to convert the chemical energy of ATP into motion. Includes dynein, kinesin, and mysoin

cytokinesis

division of the cytoplasm to form two daughter cells. Typically occurs immediately after division of the nucleus by mitosis or meiosis

cytoplasmic streaming

the directed flow of cytosol and organelles that facilitates distribution of materials within some large plant and fungal cells. Occurs along actin filaments and is powered by myosin

cell crawling

a form of cellular movement involving actin filaments in which the cell produces bulges (pseudopodia) that stick to the substrate and pull the cell forward

intermediate filament

a long fiber, about 10nm in diameter, composed of one of various proteins; one of the three types of cytoskeletal fibers. Used to form networks that help maintain cell shape and hold the nucleus in place

nuclear lamins

intermediate filaments that make up the nuclear lamina layer--a lattice-like layer inside the nuclear envelope and helping to organize the chromosomes

mircotubules

a long, tubular fiber 25 nm in diameter, formed by polymerization of tubulin protein dimers; one of the three types of cytoskeletal fibers. Involved in cell movement and transport of material within the cell

dimers

an association of two molecules that may be identical (homodimer) or different (heterodimer)

microtubule organizing cener MTOC

General term for any structure that organizes microtubules in cells

centrosome

Structure in animal and fungal cells, containing two centrioles, that serves as a microtubule organizing center for the cells' cytoskeleton and for the spindle apparatus during cell division

centrioles

one of two small cylindrical structures found together within the centrosome near the nucleus of a eukaryotic cell (not found in plants). consist of microtubule triplets and is structurally identical with a basal body

kinesin

a class of motor proteins that uses the chemical energy of ATP to "walk" toward the plus end of a microtubule. Used to transport vesicles, particles, organelles and chromosomes

cilia

One of many short, filamentous projections of some eukaryotic cells, containing a core of microtubules. used to move the cell as well as to circulate fluid or particles around the surface of a stationary cell

axoneme

a structure found in eukaryotic cilla and flagella and responsible for their motion; composed of two central microtubules surrounded by nine doublet microtubules (9+2 arrangement)

basal body

the microtubule organizing center for cilia and flagella in eukaryotic cells. Consists of nine triplets of microtubules arranged in a circle and establishes the structure of axonemes. structurally identical with a centriole

dynein

a class of motor proteins that uses the chemical energy of ATP to "walk" toward the minus end of a microtubule. dyneins are responsible for bend of cilia and flagella, play a role in chromosome movement during mitosis, and can transport vesicles and organelles

free energy

the energy of a system that can be converted into work. It may be measured only through the change in free energy in a reaction

kinetic energy

the energy of motion

potential energy

energy stored in matter as a result of its position or molecular arrangement

first law of thermodynamics

the principle of physics that energy is conserved in any process. Energy can be transferred and converted into different forms, but I cannot be created or destroyed

enthalpy

(H) a quantitative measure of the amount of potential energy, or heat content, of a system plus the pressure and volume it exerts on its surroundings

exothermic

referring to a chemical reaction that releases heat

endothermic

referring to a chemical reaction that absorbs heat

entropy

(S) a quantitative measure of the amount of disorder of any system, such as a group of molecules

second law of thermodynamics

the principle of physics that the entropy of the universe or any closed system always increases

Gibbs free-energy change

a measure of the change in enthalpy and entropy that occurs in a given chemical reaction. Delta G is less than 0 for spontaneous reactions and greater than 0 for nonspontaneous reactions

exergonic

referring to a chemical reaction that can occur spontaneously, releasing heat and/or increasing entropy, and for which the Gibb free-energy change (Delta G) is less than 0

endergonic

referring to a chemical reaction that requires an input of energy to occur and for which the Gibbs free energy change (Delta G) is greater than 0

energetic coupling

in cellular metabolism, the mechanism by which energy released from an exergonic reaction (commonly, hydrolysis of ATP) is used to drive an endergonic reaction

reduction-oxidation reactions (redox reactions)

any chemical reaction that involves either the complete transfer of one or more electrons from one reactant to another, or a reciprocal shift in the position of shared electrons within one or more of the covalent bonds of two reactants

oxidation

the loss of electrons from an atom or molecule during a redox reaction, either by donation of an electron to another atom or molecule, or by the shared electrons in covalent bonds moving farther from the atomic nucleus

reduction

the gain of electrons by an atom or molecule during a redox reaction, either by acceptance of an electron form another atom or molecule, or by the shared electrons in covalent bonds moving closer to the atomic nucleus

flavin adenine dinucleotide (FAD/FADH2)

Oxidized and reduced forms, respectively, of flavin adenine dinucleotide. A nonprotein electron carries that function in the citric acid cycle and oxidative phosphorylation

electron carrier

any molecule that readily accepts electrons from and donates electrons to other molecules. Protons may be transferred with the electrons in the form of hydrogen atoms

nicotinaminde adenine dinucleotide (NAD+)

a non protein carrier that is reduced during the light-dependent reaction in photosynthesis and extensively used in biosynthetic reactions

NADH

a non protein carrier that is reduced during the light-dependent reaction in photosynthesis and extensively used in biosynthetic reactions

adenosine triphosphate (ATP)

a molecule consisting of an adenine base, a sugar, and three phosphate groups that can be hydrolyzed to release energy. Universally used by cells to store and transfer energy

kilocalorie

a unit of energy often used to measure the energy content of food. a kcal of energy raises 1 kg of water 1 degree C

substrate

1) a reactant that interacts with a catalyst, such as an enzyme or ribozyme, in a chemical reaction
2) a surface on which a cell or organism sits

phosphorylation

Addition of a phosphate group.

catalysts

any substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change

active site

the location in an enzyme molecule where substrates (reactant molecules) bind and react

transition state

a high-energy intermediate state of the reactants during a chemical reaction that must be achieved for the reaction to proceed

Enzyme catalysis can be analyzed as a three step process:

Initiation
Transition state Facilitation
Termination

Initiation

1) in an enzyme-catalyzed reaction, the stage during which enzymes orient reactant precisely as the bind at specific location within the enzyme's active site
2) In DNA transcription, the stage suring which RNA polymerase and other proteins assemble at the promoter sequence and open the strands of DNA to start transcription
3) In translation, the stage during which a complex consisting of initiation factor proteins, a ribosome, and mRNA and an aminoacyl tRNA corresponding to the start codon is formed

Transition state facilitation

the second stage (after initiation) in enzyme-catalyzed reactions, in which the enzyme enables formation of the transition state

termination

1) in enzyme-catalyzed reactions, the final stage in which the enzyme returns to its original conformation and products are released.
2) in transcription, the dissociation of RNA polymerase from DNA
3) in translation, the dissociation of a ribosome from mRNA when it reaches a stop codon

Cofactors

an inorganic ion, such as a metal ion, that is required for an enzyme to function normally. May be bound tightly to an enzyme or associate with it transiently during catalysis

Coenzymes

a small organic molecule that is a required cofactor for an enzyme-catalyzed reaction. often donates or receives electrons or function groups during the reaction

prosthetic groups

a non-amino acid atom or molecule that is permanently attached to an enzyme or other protein and is required for its function

competitive inhibition

inhibition of an enzyme's ability to catalyze a chemical reaction via binding of a nonreactant molecule that competes with the substrate(s) for access to the active site

allosteric regulation

regulation of a protein's function by binding of regulatory molecule, usually to a specific site distinct from the active site, that causes a change in the protein's shape

feedback inhibition

a type of control in which high concentrations of the product of a metabolic pathway inhibit one of the enzymes early in the pathway. A form of negative feedback

bioremediation

the sue of living organisms, usually bacteria or archaea, to degrade environmental pollutants

catablic pathways

any set of chemical reaction that breaks down large, complex molecules into smaller ones, releasing energy in the process

anablic pathways

any set of chemical reaction that synthesizes large molecules form smaller ones. Generally requires an input of energy

glucose

six-carbon monosaccharide whose oxidation in cellular respiration is the major source of ATP in animal cells

glycolysis

a series of 10 chemical reactions that oxidize glucose to produce pyruvate, NADH, and ATP. used by organisms as part of fermentation or cellular respiration

oxidative phosphorylation

production of ATP molecules by ATP synthase using the proton gradient established via redox reactions of an electron transport chain

cellular respiration

a common pathway for production of ATP, involving transfer of electrons from compounds with high potential energy through an electron transport chain and ultimately to an electron acceptor (often oxygen)

homeostasis

the array of relatively stable chemical and physical conditions in an animals' cells, tissues, and organ. May be achieved by the body's passively matching the conditions of a stable external environment or by active physiological processes triggered by variation in the external or internal environments

substrate-level phosphorylation

production of ATP or GTP by the transfer of a phosphate group from an intermediate substrate directly to ADP or GDP. Occurs in glycolysis and in the citric acid cycle

phoshofructokinase

enzyme that catalyzes synthesis of fructose-1,6-biphosphate from fructose-6-phosphate, a key reaction in glycolysis

cristae

sac-like invaginations of the inner membrane of a mitochondrion. Location of the electron transport chain and ATP synthase

mitochondiral matrix

central compartment of a mitochondrion, which is lined by the inner membrane; contain mitochondrial SNA, ribosomes, and the enzymes for pyruvate processing and the citric acid cylce

coenzyme A (CoA)

a molecule that is required for many cellular reactions and that is often transiently linked to other molecules, such as acetyl groups

acetyl CoA

a molecule produced by oxidation of pyruvate (the final product of glycolysis) in a reaction catalyzed by pyruvate dehydrogenase. can enter the citric acid cycle and is used as a carbon source in the synthesis of fatty acids, steroids, and other compounds

pyruvate dehydrogenase

a large enzyme complex, located in the mitochondrial matix, that is responsible for converting pyruvate to acetyl CoA during cellular respiration

citric acid cycle

a series of eight chemical reactions that start with citrate (deprotonated citric acid) and ends with oxaloacetate, which reacts with acetyl CoA to form citrate--forming a cycle that is part of the pathway that oxidizes glucose to CO2. Also known as the Krebs cycle or tricarboxylic acid (TCA) cycle

guanosine triphoshpate (GTP)

a nucleotide consisting of guanine, a ribose sugar, and three phosphate groups. Can be hydrolyzed to release free energy. Commonly used in RNA synthesis and also function in signal transduction is association with G proteins

electron transport chain (ETC)

any set of membrane-bound protein complexes and mobile electron carries involved in a coordinated series of redox reactions in which the potential energy of electrons is successively decreased and used to pump protons from one side of the membrane to the other

ubiquinone/co enzyme q

a nonprotien molecule that shuttles electrons between membrane-bound complexes in the mitochondrial electron transport chain

cytochrome c

a soluble protein that shuttles electrons between membrane-bound complexes in the mitochondrial electron transport chain

chemiosmosis

an energetic coupling mechanism whereby energy stored in an electrochemical proton gradient is used to drive an energy-requiring process such as production of ATP

proton-motive force

the combined effect of a proton gradient and an electric potential gradient across a membrane, which can drive protons across the membrane. used by mitochondria and chloroplasts to power ATP synthesis via the mechanism of chemiosmosis

aerobic

referring to any metabolic process, cell or organism that uses oxygen as an electron acceptor

anaerobic

referring to any metabolic process, cell, or organism that uses an electron acceptor other than oxygen, including fermentation or anaerobic respiration

Fermentation

any of several metabolic pathways that regenerate oxidizing agents, such as NAD+, by transferring electrons to a final electron acceptor in the absence of an electron transport chain. Allows pathways such as glycolysis to continue to make ATP

lactic acid fermentation

catabolic pathway in which pyruvate produced by glycolysis is converted to lactic acid in the absence of oxygen

alchohol fermentation

catabolic pathway in which pyruvate produced by glycolysis is converted to ethanol in the absence of oxygen

facultative anaerobes

any organism that can survive and reproduce by performing aerobic respiration when oxygen is available or fermentation when it is not

photosynthesis

the complex biological process that converts the energy of light into chemical energy stored in glucose and other organic molecules. Occurs in most plants, algae, and some bacteria

autotrophs

any organism that can synthesize reduced organic compounds from simple inorganic sources such as CO2 or CH2.l Most plants and some bacteria and archaea are autotrophs.

heterotrophs

any organism that cannot synthesize reduced organic compounds from inorganic sources and that must obtain them from other organisms. Some bacteria, some archaea, and virtually all fungi and animals are heterotrophs

Calvin cycle

in photosynthesis, the set of reaction s that use NADPH and ATP formed in the light-depended reaction to drive the fixation of CO2 reduction of the fixed carbon to produce sugar, and the regeneration of the substrate used to fix CO2. Also called light-independent reactions

NADP+ (nicotinamide adenine dinucleotide phosphate)

Oxidized and reduced forms, respectively, of nicotinamids adenine dinucleotide phosphate. A nonprotein electron carrier that is reduced during the light-dependent reaction in photosynthesis and extensively used in biosynthetic reactions

chloroplasts

a chlorophyll-containing organelle, bounded by a double membrane, in which photosynthesis occurs; found in plants and photosynthetic protists. also the location of starch, amino acid, fatty acid, purine, and pyrimidine synthesis

thylakoids

a membrane-bound network of flattened sac-like structures inside a plant chloroplast that function in converting light energy to chemical energy. a stack of thylakoid discs is a granum

grana

in chloroplasts, a stack of flattened, membrane-bound thylakoid discs where the light reactions of photosynthesis occur

stroma

the fluid matrix of a chloroplast in which the thylakoids are embedded. site where the Calvin cycle reactions occur

pigments

any molecule that absorbs certain wavelengths of visible light and reflects or transmits other wavelengths

wavelenth

the distance between two successive crests in any regular wave, such as light waves, sound waves, or waves in water

elecrtomagnetic spectrum

the entire range of wavelengths of radiation extending from short wavelengths (high energy) to long wavelengths (low energy). Includes gamma rays, X-rays, ultraviolet, visible light, infrared...

visible light

the range of wavelengths of electromagnetic radiation that humans can see, from about 400 to 700 nm

photons

a discrete packet of light energy; a particle of light

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